When the last unit in a higher hierarchy (i.e. battalion level) was destroyed by the enemy, all subordinate formations became invisible, i.e. not listed in the Ground Forces window or the GU/Stockpiles tab. I can only see the units still exist because 1) They're still killing and dying, and 2) I can load them into troop transports and unload them again, but that doesn't make them visible again.
Note in case it matters, playing a 2.4.0 game that I manually upgraded to 2.5.0 per instructions from Steve.
EDIT: I tried loading them into the ships, then toggling on "Show Ships" in the OOB, selecting them while they were in the ship, clearing hierarchy for each unit, and then unloading back onto the planet. That did the trick, I can now see them in the normal OOB again. Seems like the intended behavior when a superior formation is killed should be to either move up a level in the hierarchy or fall out of the hierarchy to be at the level of the local population.